10. Ancillary tools

10.1. crate_docs

Launches this documentation via your web browser.

10.2. crate_make_demo_database

Options as of 2016-07-21:

usage: crate_make_demo_database [-h] [--size {0,1,2,3}] [--verbose] [--echo]
                                [--doctest-doc DOCTEST_DOC]
                                [--doctest-docx DOCTEST_DOCX]
                                [--doctest-odt DOCTEST_ODT]
                                [--doctest-pdf DOCTEST_PDF]
                                url

positional arguments:
  url                   SQLAlchemy database URL. Append ?charset=utf8, e.g. my
                        sql+mysqldb://root:password@127.0.0.1:3306/test?charse
                        t=utf8 . WARNING: If you get the error 'MySQL has gone
                        away', increase the max_allowed_packet parameter in
                        my.cnf (e.g. to 32M).

optional arguments:
  -h, --help            show this help message and exit
  --size {0,1,2,3}      Make tiny (0), small (1), medium (2), or large (3)
                        database (default=0)
  --verbose, -v         Be verbose (use twice for extra verbosity)
  --echo                Echo SQL
  --doctest-doc DOCTEST_DOC
                        Test file for .DOC (default: /home/rudolf/Documents/co
                        de/crate/crate_anon/anonymise/../../testdocs_for_text_
                        extraction/doctest.doc)
  --doctest-docx DOCTEST_DOCX
                        Test file for .DOCX (default: /home/rudolf/Documents/c
                        ode/crate/crate_anon/anonymise/../../testdocs_for_text
                        _extraction/doctest.docx)
  --doctest-odt DOCTEST_ODT
                        Test file for .ODT (default: /home/rudolf/Documents/co
                        de/crate/crate_anon/anonymise/../../testdocs_for_text_
                        extraction/doctest.odt)
  --doctest-pdf DOCTEST_PDF
                        Test file for .PDF (default: /home/rudolf/Documents/co
                        de/crate/crate_anon/anonymise/../../testdocs_for_text_
                        extraction/doctest.pdf)

10.3. crate_test_anonymisation

Options as of 2016-07-21:

usage: crate_test_anonymisation [-h] --config CONFIG --dsttable DSTTABLE
                                --dstfield DSTFIELD [--limit LIMIT]
                                [--rawdir RAWDIR] [--anondir ANONDIR]
                                [--resultsfile RESULTSFILE]
                                [--scrubfile SCRUBFILE] [--verbose]
                                [--pkfromsrc | --pkfromdest]
                                [--uniquepatients | --nonuniquepatients]

Test anonymisation

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file name (input) (default: None)
  --dsttable DSTTABLE   Destination table (default: None)
  --dstfield DSTFIELD   Destination column (default: None)
  --limit LIMIT         Limit on number of documents (default: 100)
  --rawdir RAWDIR       Directory for raw output text files (default: raw)
  --anondir ANONDIR     Directory for anonymised output text files (default:
                        anon)
  --resultsfile RESULTSFILE
                        Results output CSV file name (default:
                        testanon_results.csv)
  --scrubfile SCRUBFILE
                        Scrubbing information text file name (default:
                        testanon_scrubber.txt)
  --verbose, -v         Be verbose (use twice for extra verbosity) (default:
                        0)
  --pkfromsrc           Fetch PKs (document IDs) from source (default)
                        (default: True)
  --pkfromdest          Fetch PKs (document IDs) from destination (default:
                        True)
  --uniquepatients      Only one document per patient (the first by PK)
                        (default) (default: True)
  --nonuniquepatients   Documents in sequence, with potentially >1
                        document/patient (default: True)

10.4. crate_estimate_mysql_memory_usage

Options as of 2016-07-21:

usage: crate_estimate_mysql_memory_usage [-h] [--mysql MYSQL] [--host HOST]
                                         [--port PORT] [--user USER]

optional arguments:
  -h, --help     show this help message and exit
  --mysql MYSQL  MySQL program (default=mysql)
  --host HOST    MySQL server/host (prefer '127.0.0.1' to 'localhost')
  --port PORT    MySQL port (default=3306)
  --user USER    MySQL user (default=root)